Metabolic flux analysis for serine alkaline protease fermentation byBacillus licheniformis in a defined medium: Effects of the oxygen transfer rate

Çalı́k, Pınar; Çalık, Güzide; Takaç, Serpil; Özdamar, Tunçer H.

doi:10.1002/(sici)1097-0290(19990720)64:2<151::aid-bit4>3.0.co;2-u

Cited by 62 publications

(3 citation statements)

References 21 publications

(20 reference statements)

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“…The process is for an enzyme production which can be considered as a model bioprocess. To increase the enzyme yield and selectivity, depending on the regulation effect of the oxygen transfer rate, the regulation of the intracellular reaction network for the enzyme synthesis should cause good coupling of supply and demand for the amino acids. , Therefore, antifoam selection in enzyme, and more generally in protein productions compared to the other biomolecule productions, can be considered as more influential to fine-tune bioreactor performance. On the other hand, E. coli is the most widely used microorganism in the production of recombinant biomolecules.…”

Section: Discussionmentioning

confidence: 99%

Novel Antifoam for Fermentation Processes: Fluorocarbon−Hydrocarbon Hybrid Unsymmetrical Bolaform Surfactant

Çalı́k

Ileri²,

Erdinc³

et al. 2005

Langmuir

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As foaming appears as a problem in chemical and fermentation processes that inhibits reactor performance, the eminence of a novel fluorocarbon-hydrocarbon unsymmetrical bolaform (FHUB: OH(CH2)11N+(C2H4)2(CH2)2(CF2)5CF3 I-) surfactant as an antifoaming agent as well as a foam-reducing agent was investigated and compared with other surfactants and a commercial antifoaming agent. The surface elasticity of FHUB was determined as 4 mN/m, indicating its high potential on thinning of the foam film. The interactions between FHUB and the microoganism were investigated in a model fermentation process related with an enzyme production by recombinant Escherichia coli, in V = 3.0 dm3 bioreactor systems with V(R) = 1.65 dm3 working volume at air inlet rate of Q(o)/V(R) = 0.5 dm3 dm(-3) min(-1) and agitation rate of N = 500 min(-1) oxygen transfer conditions, at T = 37 degrees C, pH(o) = 7.2, and C(FHUB) = 0 and 0.1 mM, in a glucose-based defined medium. As FHUB did not influence the metabolism, specific enzyme activity values obtained with and without FHUB were close to each other; however, because of the slight decrease in oxygen transfer coefficient, slightly lower volumetric enzyme activity and cell concentrations were obtained. However, when FHUB is compared with widely used silicon oil based Antifoam A, with the use of the FHUB, higher physical oxygen transfer coefficient (K(L)a) values are obtained. Moreover, as the amount required for the foam control is very low, minute changes in the working volume of the bioreactor were obtained indicating the high potential of the use of FHUB as an antifoaming agent as well as a foam-reducing agent.

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Section: Discussionmentioning

confidence: 99%

Novel Antifoam for Fermentation Processes: Fluorocarbon−Hydrocarbon Hybrid Unsymmetrical Bolaform Surfactant

Çalı́k

Ileri²,

Erdinc³

et al. 2005

Langmuir

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“…Due to their high stability and relatively low substrate specificity, alkaline serine proteases like subtilisins are crucial additives to household detergents and the greatest share on the worldwide enzyme market [2,3]. Attempts to optimize the productivity have addressed the fermentation process [4,5], protein-engineering [3,6,7], and cellular influences on protein quality and quantity [2,8]. Since the 4.2 Mb circular genome of the type strain B. licheniformis DSM13 was published in 2004 [1,9], several genome-based studies targeting strain improvement have been performed successfully [10,11].…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

et al. 2013

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BackgroundThe production of enzymes by an industrial strain requires a complex adaption of the bacterial metabolism to the conditions within the fermenter. Regulatory events within the process result in a dynamic change of the transcriptional activity of the genome. This complex network of genes is orchestrated by proteins as well as regulatory RNA elements. Here we present an RNA-Seq based study considering selected phases of an industry-oriented fermentation of Bacillus licheniformis.ResultsA detailed analysis of 20 strand-specific RNA-Seq datasets revealed a multitude of transcriptionally active genomic regions. 3314 RNA features encoded by such active loci have been identified and sorted into ten functional classes. The identified sequences include the expected RNA features like housekeeping sRNAs, metabolic riboswitches and RNA switches well known from studies on Bacillus subtilis as well as a multitude of completely new candidates for regulatory RNAs. An unexpectedly high number of 855 RNA features are encoded antisense to annotated protein and RNA genes, in addition to 461 independently transcribed small RNAs. These antisense transcripts contain molecules with a remarkable size range variation from 38 to 6348 base pairs in length. The genome of the type strain B. licheniformis DSM13 was completely reannotated using data obtained from RNA-Seq analyses and from public databases.ConclusionThe hereby generated data-sets represent a solid amount of knowledge on the dynamic transcriptional activities during the investigated fermentation stages. The identified regulatory elements enable research on the understanding and the optimization of crucial metabolic activities during a productive fermentation of Bacillus licheniformis strains.

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“…Therefore, research efforts have been focused on the B. licheniformis subtilisin fermentation process and the resulting yield of active enzyme. A major aspect has been monitoring and improvement of bioprocess parameters such as oxygen transfer rate [4-6], pH value [7,8], inoculum quality [9] and initial glucose concentration [10], whereas other studies addressed the optimization of the fermentation medium [11,12]. Strategies for the molecular biological improvement of subtilisin [13] and its secretion [14] have been described.…”

Section: Introductionmentioning

confidence: 99%

Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production

et al. 2013

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BackgroundIndustrial fermentations can generally be described as dynamic biotransformation processes in which microorganisms convert energy rich substrates into a desired product. The knowledge of active physiological pathways, reflected by corresponding gene activities, allows the identification of beneficial or disadvantageous performances of the microbial host. Whole transcriptome RNA-Seq is a powerful tool to accomplish in-depth quantification of these gene activities, since the low background noise and the absence of an upper limit of quantification allow the detection of transcripts with high dynamic ranges. Such data enable the identification of potential bottlenecks and futile energetic cycles, which in turn can lead to targets for rational approaches to productivity improvement. Here we present an overview of the dynamics of gene activity during an industrial-oriented fermentation process with Bacillus licheniformis, an important industrial enzyme producer. Thereby, valuable insights which help to understand the complex interactions during such processes are provided.ResultsWhole transcriptome RNA-Seq has been performed to study the gene expression at five selected growth stages of an industrial-oriented protease production process employing a germination deficient derivative of B. licheniformis DSM13. Since a significant amount of genes in Bacillus strains are regulated posttranscriptionally, the generated data have been confirmed by 2D gel-based proteomics. Regulatory events affecting the coordinated activity of hundreds of genes have been analyzed. The data enabled the identification of genes involved in the adaptations to changing environmental conditions during the fermentation process. A special focus of the analyses was on genes contributing to central carbon metabolism, amino acid transport and metabolism, starvation and stress responses and protein secretion. Genes contributing to lantibiotics production and Tat-dependent protein secretion have been pointed out as potential optimization targets.ConclusionsThe presented data give unprecedented insights into the complex adaptations of bacterial production strains to the changing physiological demands during an industrial-oriented fermentation. These are, to our knowledge, the first publicly available data that document quantifiable transcriptional responses of the commonly employed production strain B. licheniformis to changing conditions over the course of a typical fermentation process in such extensive depth.

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Metabolic flux analysis for serine alkaline protease fermentation byBacillus licheniformis in a defined medium: Effects of the oxygen transfer rate

Cited by 62 publications

References 21 publications

Novel Antifoam for Fermentation Processes: Fluorocarbon−Hydrocarbon Hybrid Unsymmetrical Bolaform Surfactant

Novel Antifoam for Fermentation Processes: Fluorocarbon−Hydrocarbon Hybrid Unsymmetrical Bolaform Surfactant

RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation

Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production

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